One of the most important books that influenced Darwin, by his own account, was John Herschel's A Preliminary Discourse on the Study of Natural Philosophy(1831). Herschel was one of the leading British scientists of the age, known for his work in astronomy, geography, and scientific method. Discourse on the Study of Natural Philosophy provided a model of the interplay between observation (experience) and theory. Herschel insisted that laws govern nature, but these laws are often difficult to determine. Attempting to understand these laws was the ultimate goal of natural philosophy. In this, researchers could discover the fundamental truth of nature unified in a single explanation. In the Origin of Species, Darwin sought to adhere to Herschel's scientific method and argument. Darwin noted in the opening pages that he was attempting "to throw some light on the origin of species -- that mystery of mysteries, as it has been called by one of our greatest philosophers." The great natural philosopher who spoke of the "mystery of mysteries" was Herschel.

But the Origin of Species called into question what had been known about the living world, arguing that species were not immutable and that there was a continuum of life, produced by naturalistic causes. In this, Darwin's theory of evolution via natural selection challenged established thought, including some of the most prominent scientists who had influenced him. Darwin sent a copy of the Origin of Species to Herschel as a token of his admiration. To his great consternation, Darwin subsequently heard that Herschel had "called natural selection 'the law of higgledy-piggledy'."

Herschel commented publicly on natural selection in the 1861 edition of his Physical Geography of the Globe, which he sent to Darwin. In a footnote, Herschel questioned Darwin's theory, given that it suggested that variations could occur in all directions, even ones that did not directly help species adjust to their dynamic environments. Such variations, in Darwin's theory, "gave no indication of the Creator's foresight." In sharp opposition to this Herschel wrote:

We can no more accept the principle of arbitrary and casual variation and natural selection as a sufficient account, per se, of the past and present organic world, than we can receive the Laputan method of composing books (pushed à l'outrance) as a sufficient one of Shakespeare and the Principia. Equally in either case, an intelligence, guided by a purpose, must be continually in action to bias the directions of the steps of change -- to regulate their amount -- to limit their divergence -- and to continue them in a definite course. We do not believe that Mr. Darwin means to deny the necessity of such intelligent direction. But it does not, so far as we can see, enter into the formula of his law; and without it we are unable to conceive how the law can have led to the results.

Although critical and concerned with the implications of Darwin's theory -- contending that evolutionary changes required "intelligent direction" and that a special stipulation needed to be made for humans -- Herschel did note enigmatically in the end: "We are far from disposed to repudiate the view taken of this mysterious subject in Mr. Darwin's work."

Responding to Herschel on May 23, 1861 -- thanking him for sending Physical Geography and commenting on the reference to natural selection -- Darwin took issue with what he called the notion of "intelligent Design," introducing this term for the first time in its modern sense:

The point which you raise on intelligent Design has perplexed me beyond measure; & has been ably discussed by Prof. Asa Gray, with whom I have had much correspondence on the subject. . . . One cannot look at this Universe with all living productions & man without believing that all has been intelligently designed; yet when I look to each individual organism, I can see no evidence of this. For I am not prepared to admit that God designed the feathers in the tail of the rock-pigeon to vary in a highly peculiar manner in order that man might select such variations & make a Fan-tail; & if this be not admitted . . . then I cannot see design in the variations of structure in animals in a state of nature, -- those variations which were useful to the animal being preserved & those useless or injurious being destroyed.

Darwin insisted that his theory of natural selection required no recourse to "intelligent direction" or a "Higher power." Still reflecting upon Herschel's contention that "the higher law of providential arrangement" should always be noted and Asa Gray's insistence on divine guidance of variation, Darwin confided to Lyell on August 1, 1861:

But astronomers do not state that God directs the course of each comet & planet. -- The view that each variation has been providentially arranged seems to me to make natural selection entirely superfluous, & indeed takes whole case of appearance of new species out of the range of science. . . . I wonder whether Herschel would say that you ought always to give the higher providential Law, & declare that God had ordered all certain changes of level that certain mountains should arise. -- I must think that such views of Asa Gray & Herschel merely show that the subject in their minds is in Comte's theological stage of science [the first of three stages in the development of knowledge].

Darwin clearly sensed the ramifications of his materialist theory with its tacit recognition of the vast indifference of nature to human affairs. Calling into question nature as evidence of God, Darwin wrote to Asa Gray on May 22, 1860:

With respect to the theological view of the question: This is always painful to me. I am bewildered. I had no intention to write atheistically. But I own that I cannot see as plainly as others do, and as I should wish to do, evidence of design and beneficence on all sides of us. There seems to me too much misery in the world. I cannot persuade myself that a beneficent and omnipotent God would have designedly created the Ichneumonidae with the express intention of their feeding within the living bodies of Caterpillars, or that a cat should play with mice. Not believing this, I see no necessity in the belief that the eye was expressly designed. On the other hand, I cannot anyhow be contented to view this wonderful universe, and especially the nature of man, and to conclude that everything is the result of brute force. I am inclined to look at everything as resulting from designed laws, with the details, whether good or bad, left to the working out of what we may call chance.

Darwin remained steadfast in his opposition to intelligent design within the physical world, including all living beings. In a letter to Julia Wedgwood, on July 11, 1861, he distinguished his position from advocates of design: "The mind refuses to look at this universe, being what it is, without having been designed; yet, where one would most expect design, viz. in the structure of a sentient being, the more I think on the subject, the less I can see proof of design. Asa Gray and some others look at each variation, or at least at each beneficial variation (which A. Gray would compare with the rain drops which do not fall on the sea, but on to the land to fertilize it) as having been providentially designed."